[English] 日本語
Yorodumi
- EMDB-8454: Cryo-electron microscopy structure of a bovine CLC-K chloride cha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8454
TitleCryo-electron microscopy structure of a bovine CLC-K chloride channel, auxiliary (class 2) conformation
Map dataStructure of a bovine CLC-K chloride channel. Combined, unfiltered map of Class 2
Sample
  • Complex: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
    • Protein or peptide: Chloride channel protein
    • Protein or peptide: Monoclonal antibody, Fab fragment, heavy chain
    • Protein or peptide: Monoclonal antibody, Fab fragment, light chain
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsCLC / chloride channel / membrane / kidney / TRANSPORT PROTEIN
Function / homology
Function and homology information


Stimuli-sensing channels / voltage-gated chloride channel activity / chloride transport / monoatomic ion channel complex / plasma membrane
Similarity search - Function
Chloride channel ClC-K / : / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBos taurus (cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsPark E / MacKinnon R
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Jane Coffin Childs Memorial Fund61-1513 United States
CitationJournal: Nature / Year: 2017
Title: Structure of a CLC chloride ion channel by cryo-electron microscopy.
Authors: Eunyong Park / Ernest B Campbell / Roderick MacKinnon /
Abstract: CLC proteins transport chloride (Cl) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC ...CLC proteins transport chloride (Cl) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl ions passively, whereas others are secondary active transporters that exchange two Cl ions for one H. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture on the basis of sequence homology. Here we determined the structure of a bovine CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl/H transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl down its electrochemical gradient.
History
DepositionOct 26, 2016-
Header (metadata) releaseDec 28, 2016-
Map releaseJan 11, 2017-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0176
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0176
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5tr1
  • Surface level: 0.0176
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8454.png

Downloads & links

-
Map

FileDownload / File: emd_8454.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a bovine CLC-K chloride channel. Combined, unfiltered map of Class 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0176 / Movie #1: 0.0176
Minimum - Maximum-0.024342816 - 0.056552105
Average (Standard dev.)0.00012446755 (±0.0026305348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0240.0570.000

-
Supplemental data

-
Mask #1

Fileemd_8454_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: B-factor-sharpend (-120 A^2) and lowpass-filtered (4.1 Ang)

Fileemd_8454_additional_1.map
AnnotationB-factor-sharpend (-120 A^2) and lowpass-filtered (4.1 Ang)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: B-factor-sharpend (-120 A^2) and lowpass-filtered (3.9 Ang)

Fileemd_8454_additional_2.map
AnnotationB-factor-sharpend (-120 A^2) and lowpass-filtered (3.9 Ang)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A bovine CLC-K channel complexed with a monoclonal antibody fragm...

EntireName: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
Components
  • Complex: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
    • Protein or peptide: Chloride channel protein
    • Protein or peptide: Monoclonal antibody, Fab fragment, heavy chain
    • Protein or peptide: Monoclonal antibody, Fab fragment, light chain
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: A bovine CLC-K channel complexed with a monoclonal antibody fragm...

SupramoleculeName: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Fab fragment generated by proteolytic (papain) cleavage of murine IgG antibody.
Source (natural)Organism: Bos taurus (cattle)

-
Macromolecule #1: Chloride channel protein

MacromoleculeName: Chloride channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 73.521484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVRRGIRGG LDWLKRKLFC VGEDWYFLTV LGVLMALISF TMSFTVGRVV RAHKWLYREI GDSHLLRYLS WTVYPVALVS FSSGFSQSI TPFSGGSGIP ELKTILSGVV LEDYLDIKNF GAKAVGLTCT LASGSTIFLG KVGPFVHLSV MIAAYLGRVR A KATGESEN ...String:
MRVRRGIRGG LDWLKRKLFC VGEDWYFLTV LGVLMALISF TMSFTVGRVV RAHKWLYREI GDSHLLRYLS WTVYPVALVS FSSGFSQSI TPFSGGSGIP ELKTILSGVV LEDYLDIKNF GAKAVGLTCT LASGSTIFLG KVGPFVHLSV MIAAYLGRVR A KATGESEN KSKRNEMLVA GAAVGVATVF AAPFSGVLFC IEVVSSHFSV WDYWRGFFAA TCGAFMFRLL AVFNSEQETI TS LYKTSFR VEVPFDLPEI FFFVALGAIC GVASCAYLFC QRKFLGFVKT NPVLSKLMAT SKPLYSALAA LVLASVTYPP GAG RFMASR LSMREYLDSL LDHNSWALLT RQASPPWPVE PDPQNLWFEW YHPQFTIFGT LAFFLVMKFW MLILATTIPM PAGY FMPIF IFGAAIGRLL GEALSVAFPE GIVAGGVTNP IMPGGYALAG AAAFSGAVTH SISTALLAFE LTGQIVHALP VLMAV LAAN AIAQSCQPSF YDGTIIVKKL PYLPWIRGRK ISSHRVTVEH FMNRAITTLA KDTPQEEVVK VVTSTDMAEY PLVAST ESQ TLVGTMRRAQ LVQALQAEPP SWAPGQQRCL QDILAEGCPV EPVTLKLSPE TSLHQAHNLF ELLNLQSLFV TSQGRAV GF VSWVELEKAI SKLTNPPAPK SNSLEVLFQ

UniProtKB: Uncharacterized protein

-
Macromolecule #2: Monoclonal antibody, Fab fragment, heavy chain

MacromoleculeName: Monoclonal antibody, Fab fragment, heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.633068 KDa
SequenceString:
DVQLQESGPG LVKPSQSLSL TCTVTGDSVT SDYAWSWIRQ FPGKKLEWMG YITYSGNTIY NPSLKSRISI TRDTSKNQFF LQLKSVIIE DTATYYCSRG VDYWGQGTSV TVSS

-
Macromolecule #3: Monoclonal antibody, Fab fragment, light chain

MacromoleculeName: Monoclonal antibody, Fab fragment, light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.824102 KDa
SequenceString:
DIVMTQSPKF MSTSVGDRVS VTCKASQNVG TNVAWYQQKP GQSPKTLIYW ASYRYSGVPD RFTGSGSGTD FTLAISNVQS EDLAEYFCQ QYNSYPLTFG SGTKLELK

-
Macromolecule #4: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris
1.0 mMC4H10O2S2DL-dithiothreitol
0.04 %C24H46O11n-dodecyl-beta-D-maltoside
0.004 %C3H50O4cholestery hemisuccinate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 0.3 sec. / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Details: generated from EMAN2 and 2D averages of particle images
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4)
Details: the indicated resolution was estimated on the primary map using the provided mask including Fab.
Number images used: 67475
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more